Thais H de Palma, Chris Powers, Morgan J McPartland, Jessica Mark Welch, Matthew Ramsey
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Using transposon insertion sequencing (TnSeq) with a highly saturated <i>mariner</i> transposon library in two strains, the ATCC33392 type-strain (<i>Hp</i> 392) and oral isolate EL1 (<i>Hp</i> EL1), we show that the essential genomes of <i>Hp</i> 392 and <i>Hp</i> EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for <i>Hp</i> 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of <i>H. parainfluenzae</i> in differing oxygen conditions, similar to its <i>in vivo</i> habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCE<i>Haemophilus parainfluenzae</i> is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. <i>H. parainfluenzae</i> correlates with good oral health and may play a role in preservation of healthy host status. Also, <i>H. parainfluenzae</i> can cause opportunistic infections outside of the oral cavity. To date, little is known about how <i>H. parainfluenzae</i> colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. 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引用次数: 0
摘要
副流感嗜血杆菌(Hp)是一种革兰氏阴性菌,在人类口腔中高度流行且数量众多,是一种不常见的口腔外机会性病原体。Hp 在口腔中占据多种生境,包括龈上菌斑生物膜。人们对 Hp 在健康的生物膜中如何与其周围环境相互作用以及它作为机会性病原体的致病机制知之甚少。为了解决这个问题,我们在体外有氧和无氧生物膜中鉴定了基本基因组和条件基本基因。通过对 ATCC33392 型菌株(Hp 392)和口腔分离株 EL1(Hp EL1)这两种菌株的高饱和度海洋转座子文库进行转座子插入测序(TnSeq),我们发现 Hp 392 和 Hp EL1 的基本基因组分别由 395 个(20%)和 384 个(19%)基因组成。核心基本基因组由 341 个(17%)基本基因组成,在两个菌株之间是一致的,由与遗传信息处理、碳水化合物、蛋白质和能量代谢相关的基因组成。我们还发现了有氧和厌氧生物膜生长的条件性必需基因,这些基因在两种菌株中都与碳水化合物和能量代谢有关。RNAseq 分析表明,厌氧生长过程中上调的大多数基因对 Hp 392 的厌氧生存并不重要。该文库的完成以及在这些条件下进行的分析使我们对副流感病毒在不同氧气条件下的基本生物学特性有了基本的了解,这与其在体内的生存环境相似。该文库为研究与人类口腔栖息地中许多微生物物种密切接触的生物体的条件性基本基因提供了一个宝贵的工具。副流感嗜血杆菌与良好的口腔健康息息相关,并可能在保持健康宿主状态方面发挥作用。此外,副流感病毒还可在口腔外引起机会性感染。尽管副流感嗜血杆菌是人类微生物组中如此常见和丰富的一部分,但迄今为止,人们对其如何在人类宿主中定植还知之甚少。在这里,我们展示了一种强大工具--TnSeq 文库--的创建和使用,该文库可用于鉴定该生物完全生长所必需的基因,以及在不同氧气状态下生长所必需的条件基因,而这正是该生物在人类宿主中可能遇到的情况。这一工具和这些数据为进一步研究这种可能在保护人类健康方面发挥作用的相对未知的生物体奠定了基础。
Essential genes for Haemophilus parainfluenzae survival and biofilm growth.
Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.
mSystemsBiochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
10.50
自引率
3.10%
发文量
308
审稿时长
13 weeks
期刊介绍:
mSystems™ will publish preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ will welcome submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ will provide streamlined decisions, while carrying on ASM''s tradition of rigorous peer review.